Friday, September 30, 2005

In fairness, there are some adherents of ID that believe in evolution, just not the start of it.

True enough.

Certainly, Michael Behe has stated in his book, Darwin's Black Box, that he accepts the notion of common descent. His issue has to do with the molecular machinery within the cell; he claims it's too complicated to have arisen by the known mechanisms in evolution.

A big problem with Bill's statement lies in the definition of "the start of it". In other words, there are adherents of ID who believe life has evolved, but that evolution can't account for the emergence of the first living thing.

One of the most popular responses is that the study of evolution deals with how life has changed since the first living thing came to be. The study of how life came to exist in the first place is abiogenesis.

This misses the point because the adherents of ID, and those who question how "evolution" accounts for the beginning of life, aren't referring to the specifics of evolutionary theory.

What they're referring to is the larger notion that the origin of life can ever be pinned down to purely naturalistic causes. In essence, they doubt that any natural process can ever, without guidance, produce a living thing out of nonliving matter.

The claim Behe argues in his book is that evolutionary processes are incapable of putting together an intricate system like the bacterial flagellum, the blood clotting cascade, or any number of other systems found in living cells. Because he rules out evolution, he argues, the causitive agent must have been something else.

Since the argument against "evolution" so often morphs into an argument against "naturalistic causes", the only alternative remaining is the supernatural. This, by definition, is beyond the reach of science.

So, my challenge to the adherents of ID/IOT is: What supernatural process is required in the development of the first living thing, what positive evidence is there to support the existence of such a supernatural process, and how can we test for the existence of such a process?

If we can't test this supernatural process, it's not science and we can't teach it in science classes.

I first encountered Tammy Bruce when her show occupied the time slot following the Saturday repeat of Rush Limbaugh. She succeeded Bill Press, former chairman of the California Democratic Party, in that time slot.

In contrast to Bill Press, Tammy was not predictable. She is a lesbian feminist and a former head of the California chapter of NOW. You could make a pretty good guess about her position on a topic, but many times, you'd guess wrong.

Bill Press was utterly predictable, and could be summed up in three words – Rush Is Wrong. If Rush said it, the opposite was true. If Rush did it, the opposite was good and worthy. If any caller offered anything at all in support of Rush's position (such "support" included anything that might argue against Bill's position), the caller was talked over, pummeled with straw-man arguments, or mocked and hung up on.

Tammy, on the other hand, gave ideas serious consideration. Sure, she has a bias, but it's not a prison. As a result, she wrote The New Thought Police, denouncing the ways the Lunatic Left has attacked people who argue against them rather than making a resoned case. With that book, she became an honorary Conservative. (So much for "dissent is patriotic"!)

I don't always agree with her, but I always find her worth listening to.

Monday, September 26, 2005

Remember all those people we heard about dying in the Superdome during hurricane Katrina?

I guess they must have gotten better. (HT: Clayton Cramer)

Following days of internationally reported killings, rapes and gang violence inside the Dome, the doctor from FEMA - Beron doesn't remember his name - came prepared for a grisly scene: He brought a refrigerated 18-wheeler and three doctors to process bodies.
"I've got a report of 200 bodies in the Dome," Beron recalls the doctor saying.
The real total was six, Beron said.

If the same ratio applies to the initial guesstimates of 10,000 dead, the real number is closer to 300.

Back on September 6, I quoted a number of news stories with horrifying first-hand accounts, quoting identifiable eyewitnesses. I am deeply troubled by this: either reporters were making stuff up, or they were quoting liars--and multiple liars who told roughly similar stories of what was going on in the Superdome--or there's a coverup going on now. Either way, this doesn't speak well for the journalism profession.

A conspiracy theorist might even suspect that stories casting a bad light on the feds in general, and President Bush in particular, are subject to less fact-checking and examination than is typical for other stories.

One scientist came up with a new way of explaining how biology works. A generation later, the other one came up with a new way of explaining how physics works.
Today, after a century of scrutiny, both explanations still pretty much hold up. But in popular culture, physicist Albert Einstein is idolized, while biologist Charles Darwin's legacy is clouded with controversy.

In his highly influential book "The Structure of Scientific Revolutions," science philosopher Thomas Kuhn presented the idea that science is not a gradual progression toward truth, but a series of insurgencies, with scientific theories constantly usurping one another.
That is sometimes true. And proponents of intelligent design love Kuhn's argument.

After examining ID's two main arguments, the answers to the original questions — what does ID offer? And what can ID explain that evolution can't? — is not much and nothing, leading scientists say.
"The most basic problem [with ID] is that it's utterly boring," said William Provine, a science historian at Cornell University in New York. "Everything that's complicated or interesting about biology has a very simple explanation: ID did it."

And just to make matters worse, where Intelligent Design does make predictions, they're wrong.

In 1975, Japanese scientists discovered a bacterium that can eat nylon. That is, a bacterium with specialized enzymes that break down and extract nourishment from a molecule that didn't exist before 1935.

The discovery of nylon-eating bacteria poses a problem for ID proponents. Where did the CSI [Complex Specified Information] for nylonase—the actual protein that the bacteria use to break down the nylon—come from?
There are three possibilities:

The nylonase gene was present in the bacterial genome all along.

The CSI for nylonase was inserted into the bacteria by a Supreme Being.

The ability to digest nylon arose spontaneously as a result of mutation. Because it allowed the bacteria to take advantage of a new resource, the ability stuck and was eventually passed on to future generations.

Apart from simply being the most reasonable explanation, there are two other reasons that most scientists prefer the last option, which is an example of Darwinian natural selection.
First, hauling around a nylonase gene before the invention of nylon is at best useless to the bacteria; at worst, it could be harmful or lethal. Secondly, the nylonase enzyme is less efficient than the precursor protein it's believed to have developed from. Thus, if nylonase really was designed by a Supreme Being, it wasn't done very intelligently.

Friday, September 23, 2005

The cases are now legion in which confidential e-mails are getting hung out to dry like so much dirty linen. Executives have been embarrassed on the witness stand (Bill Gates), fired (Harry Stonecipher) and ordered off to jail (Frank Quattrone) for hitting the "send" button after typing something inappropriate for public consumption.

People have taken the advice to back up their data to heart. Even if you delete your mail and scrub the disk, backup copies abound. And so do opportunities.

One company's legal headache is another's livelihood. A Marsh & McLennan subsidiary, Kroll Ontrack, is in the business of helping lawyers find needles in haystacks. A recent assignment had it helping a corporation respond to a government antitrust inquiry by sorting 3.5 terabytes (3.5 trillion characters) of electronic documents, roughly half of them e-mail, so that an army of lawyers, working three shifts a day, 450 at a time, could probe them for telltale words.

One safeguard would be to encrypt your e-mail. Then, just hope the recipient doesn't archive it or forward it in the clear.

One of the scares that have been floating around is that the use of antibacterial soap might breed resistant bacteria.

Researchers from the University of Michigan, Tufts University and Columbia University studied 224 households to determine whether household use of antibacterial cleaning and hygiene products is an emerging risk factor for the carriage of antibiotic-resistant bacteria (search) on the hands.
The researchers randomly assigned the households to use either antibacterial or non-antibacterial soap and cleaning products for one year. The active ingredient in the antibacterial products was triclosan (search), which has been found to be effective in reducing and controlling bacterial contamination when used properly.
The researchers reported in the October issue of Emerging Infectious Diseases that, “The results from our study do not implicate use of antibacterial cleaning and hygiene products as an influential factor in the carriage of anti-microbial drug-resistant bacteria on the hands of household members.”

Problem is, their testing found antibacterial soap wasn't any better at controlling bacteria than good old soap and water.

Thursday, September 22, 2005

In another long piece, I examine the "scientific alternative" Intelligent Design / Intelligent Origin Theory (ID/IOT). How scientific is it?

In part I, I look at the rules science has to follow in order to be called "science". (I also complain about how kids these days are not being taught science – they're being taught about science.)

In part II, I look at how well evolution measures up against the rules of science. Conclusion: pretty well.

I think, part IV is going to discuss meaning. A big objection to evolutionary science is that it seems to remove meaning and purpose from life. If all the exquisite design we see arose from the blind, undirected operation of natural law, where is intelligence, and meaning?

In the face of pressure to withdraw from Iraq, it looks like we may still need to stay – for at least a while longer.

The rapidity of the democratization and reform of Iraq is staggering. There was no German state for four years after the Second World War. By contrast, Iraq has moved from a centralized, one-man dictatorship to a decentralized, federal republic in half that time.

American forces are in Iraq at the invitation of the democratically elected government of Iraq, and with the backing of a United Nations Security Council resolution. Your soldiers are in my country because of your commitment to democracy. Moreover, during my visit to Washington, Mr. Bush reaffirmed the United States' complete support for the Iraqi political process toward sustainable democracy, and for the fight to defeat fascist and jihadist terrorism in Iraq.

US forces are doing more than just mopping up in Iraq, too. They're preventing local wars, both inside and outside Iraq.

Americans should be proud of what its soldiers have achieved. The presence of foreign forces has prevented a renewed civil war in Iraq--renewed because there has already been a civil war in Iraq. For 35 years, Saddam and his Baath Party made war on the Iraqi people. The liberation of Iraq ended that civil war.

Above all, American forces provide Iraq with a much-needed deterrence capability. In the past, Iraq sought an illusory security through the follies of aggression, terrorism and weapons of mass destruction. Today, our external security comes from our alliance with the United States. Our neighbors can thereby be assured that we will settle all of our differences with them peacefully.

People who have spoken out against affirmative action have been accused of wanting to pull the ladder up after them, now that they've achieved their success. I won't suggest the people who want us out of Iraq have the same mind set – we've got our security, now we won't lift a finger to help others achieve theirs.

I attempted to get a sense of his temperament and values. And I asked him about the end-of-life decisions: clearly, decisions that are gut-wrenching, difficult and extremely personal. Rather than talking to me as a son, a husband, a father--which I specifically requested he do--he gave a very detached response.

This seems to be the same problem people have with the Federal response to Hurricane Katrina, and especially Bush's performance.

It boils down to the word "performance", as in drama.

Debates over how effective the federal response was, and who was supposed to be in charge in the first place completely miss the point.

What the left wanted was a president who would cry. Once a president sheds that tear, and speaks with that quaver in his voice, he's done all he needs to do. After he proves he cares, response can take as long as it likes. The people who live long enough to see it will know he cares, or if they protest the delay, they'll be shouted down. ("Fool! Can't you see he cares?")

On the other hand, you can have the best response in the world, and if all you do is have help there when it's needed, but show no emotion, you're branded as uncaring, and everything that goes wrong is laid at your door.

Maybe all Bush needs is a heart transplant –'; from his chest to his sleeve.

Under the headline of "The Reporters Who Didn't Bark", Hugh Hewitt notes a gap in coverage of California's bill which would allow same-sex marriages. He's been unable to find any Democratic leader who's been quoted on the bill.

National news media accounts of the votes and the vetoes quoted the backers of the proposal as well as the governor's spokespeople, and advocates and opponents on both sides of the debate.
But in no story that I can find did a reporter think to ask a national Democratic leader for their opinion on the vote by their California colleagues. Google News cannot even find San Francisco Democrat and House minority leader Nancy Pelosi's name in the same story as same-sex marriage. Neither can the San Francisco Chronicle over the past 30 days.

Maybe they don't care about it.

Or, if you're of a conspiratorial turn of mind, maybe reporters don't want certain questions, and their answers, on the record.

How to explain the media's collective pass issued to big-name Dems?
Simple enough: They are sparing them a series of questions that would embarrass them. Such as:
"Senator Clinton, the California Democrats have pushed through a same-sex marriage bill. Should Governor Schwarzenegger sign it?"
"I need to follow up on that senator. I realize it is a local issue, but it has national implications, senator. Does it make sense to you?"
"If the bill is signed and the Defense of Marriage Act fails to prevent mandatory recognition of California marriages in states that have rejected the idea, should the Constitution be amended to provide for a state option or even a total ban?"
"Isn't the California Democratic party really reflecting the true feelings of the Democrats, feelings which a number of your colleagues share but which come with too high a political penalty?"

Monday, September 19, 2005

Last night, my girlfriend and I were pondering what was worth watching on TV. I vetoed watching "Sixty Minutes", on the grounds that I didn't feel like arguing over the material they would present. (We watched the second installment of "Rome" instead – quite good, by the way.)

In retrospect, I'm glad I skipped Sixty Minutes.

One of the segments presented a bleak view of life in Iraq:

Tonight (Sunday, September 18, 2005), 60 Minutes aired a segment entitled "Life in Baghdad," hosted by Scott Pelley and produced by Shawn Efran. The story was nothing but the bleakest of portraits of life in the city of Baghdad. The story? Violence, fear, despair: repeat.
However, unless you were paying close attention to Pelley's introduction to the story, you may have missed the fact that the segment originally aired nearly one year ago (On 60 Minutes II, October 6, 2004)! ("Last fall," as host Pelley put it.)
Well, a lot has happened since last fall! Free elections! A stronger Iraqi security force! A forthcoming constitution!
Has life improved in Baghdad since last year? 60 Minutes doesn't want to tell us. (On the other hand, if they don't want to tell us, that could be a sign that things are getting better.)

A customer called in to find out whether she had hard water where she lives. It turns out she's taking medication and if she's got hard water, it's been suggested that she take it with distilled water.

I told her she gets "medium" (by industry standards) water, and asked her what medication it was. It turns out to be the generic form of Fosamax, a treatment for osteoporosis.

I gave her the numbers for the hardness in her area, and suggested she run it past her pharmacist to verify this was soft enough. She said the advice was even news to her pharmacist.

So I went Googling.

Looking under "Fosamax", "water", and "hardness", I found a document that gave me the scoop. The link has since moved, so I used the cached version.

Medication Absorption with Hard Water
Reminder: If your community has hard water, you may want to consider advising your patients to use distilled water when taking specific medications.
The absorption of some drugs is affected by the hardness of water. For instance, the patient insert for Fosamax® (alendronate sodium) states that “because of high mineral content, ‘hard water’ may decrease absorption of FOSAMAX. If your normal drinking water is classified as ‘hard water,’ you should consider taking this medication with distilled water (i.e. not mineral water).”
The pharmacist who reminded us of this issue contacted Merck Frosst and was advised that, since only a small amount of Fosamax is absorbed by the body, any further decrease in absorption could have a significant impact on the efficacy of the drug.
Environment Canada has defined soft and hard water as:

very soft water 0 to 60 ppm. calcium carbonate

less soft water 61 to 120 ppm. calcium carbonate

hard water 121 to 180 ppm. calcium carbonate

very hard water > 180 ppm. calcium carbonate

This does not mean all the calcium in your water has to be carbonate to count as hardness – it's typical to calculate hardness as if all the calcium found were the carbonate salt.

It occurs to me, if the serum concentration of the drug is that sensitive to hardness, you might want to take the pills with distilled water anyway. And don't take any Tums or any other calcium-basd antacids within about an hour of taking the pills, either.

And of course, no milk or cheese, or other calcium-rich foods during that time, as well.

What we need here is some real numbers on how much of an effect dietary calcium has on the serum concentration of the drug. It might be this is an effect that is what I call "significant but not useful". It shows up in the lab under analysis, but is otherwise swamped in the normal variation that appears in daily life.

I'm going to speculate that it won't make any real difference. However, it might make people feel better if they make these minor changes in their lives.

Friday, September 16, 2005

Jeff Jacoby's not the only one to notice: There's a slander making the rounds in society.

The slimy and toxic water covering much of New Orleans does not stink nearly as much as the slimy and toxic accusation that help didn't reach the victims of Hurricane Katrina quickly enough because most of those victims were black.

And in the echo chamber that is the mainstream media, it gets repeated over and over.

Jesse Jackson [...alleged] that when churches were contacted about helping some of the victims, the first thing they wanted to know was, "Are they black or white?"

Rapper Kanye West went on a tirade during NBC's hurricane relief telethon. ... The arrival of National Guardsmen in New Orleans meant that "they've given them permission to go down and shoot us. . . . George Bush doesn't care about black people."

(While I'm thinking of it, did I hear Cindy Sheehan refer to the National Guard in New Orleans as "occupiers"?)

Last night, at dinner, a lady at the table shared her opinion that help was delayed because Bush hates black people. When I pointed out what a slimy thing that was to say, she told me she didn't want the discussion to descend into name-calling.

Excuse me?

Ex-cuuuuuuuuse me?????

She lost the right to complain about name calling when she led off by calling Bush racist.

(Amusingly, her defense was, "I didn't call him racist, I said he hates blacks.")

Oh. That clears it up. And the KKK wasn't racist, either.

Even though superficially directed only at one person, the claim that help arrived late because Bush hates blacks slanderes huge numbers of people. It is a slander against:

Everyone in the Administration who carries out Presidential orders

Everyone in FEMA

Everyone in Homeland Security

Everyone in the National Guard who had any decision-making authority.

Everyone who supports George W. Bush (either so evil they don't mind supporting a racist, or so stupid they didn't see him for what he is).

Sorry, you can't issue forth a broadside like that and then pieously claim, "I don't want to see this descend to name-calling." If you seriously object to name-calling, you need to withdraw that racism charge and apologize for it. Otherwise, you've opened the door to that level of attack.

Wednesday, September 14, 2005

Gene changes related to brain size occurred sometime between 5800 years ago and 37,000 years ago. Modern humans came into existence some 200,000 years ago. That means the brain was still evolving in significant ways well after the development of the genus Homo. (During the last 9-19% of the time the genus has been around.)

The linked article explains the steps involved in arriving at this conclusion, and it's an interesting read. Among other things, it seems to follow that the process of brain evolution is by no means at a standstill – we can predict further changes will take place in the next few thousand years. (We might even be right!)

However, it's worth looking at the titles in the "references" section. These include "Reconstructing the evolutionary history of microcephalin, a gene controlling human brain size", and "Adaptive evolution of ASPM, a major determinant of cerebral cortical size in humans", both published in Human Molecular Genetics.

Notice what's going on in these articles. Evolution is not being proven in these articles – it's assumed as a fundamental process on which further research is based.

Research articles assume Newton's laws and the laws of thermodynamics without seeing the need to re-establish them, even though they're "just theories". Real science treats evolution the same way. Any "debate" over whether evolution is real exists only at the political level.

Tuesday, September 13, 2005

An eavesdropper can tell what someone is typing from the sound the keyboard makes.

The idea is that different keys tend to make slightly different sounds, and although you don't know in advance which keys make which sounds, you can use machine learning to figure that out, assuming that the person is mostly typing English text. (Presumably it would work for other languages too.)

the recognizer bootstrapped this way can even recognize random text such as passwords: In our experiments, 90% of 5-character random passwords using only letters can be generated in fewer than 20 attempts by an adversary; 80% of 10-character passwords can be generated in fewer than 75 attempts. Our attack uses the statistical constraints of the underlying content, English language, to reconstruct text from sound recordings without any labeled training data.

Soon, high-security keyboards will have to generate spurious noises that mimic the sounds of keys. Maybe it would suffice to record the sound of a key being struck, and replicate it some number of times sith some random delay between iterations.

It might still be possible to work out the mapping between the sounds and the keys, but it should still be very hard to work out which keys are being struck precisely when.

From a comment to Bruce's post: One of those projection keyboards, which projects a keyboard layout onto a convenient flat surface and detects where your fingers hit, would also circumvent this attack. You might want to program the display to black out and shift to a slightly different location every few minutes.

Byron York reports on a poll asking what people think "privacy" means.

In anticipation of the Roberts hearings, Republican pollster David Winston asked a question to measure public sentiment on one of the most contentious issues to come up in the sessions:

When you think of the right to privacy, what comes closer to how you think of that right?
A) The right to be free from government intrusion -- including private phone calls, private mail, private medical and financial information, and the right to raise your children as you see fit.
B) The right to make decisions free from government interference, such as the right to choose abortion.

The results:

Respondent

A
Freedom from government intrusion

A
Freedom from government interference

A
No opinion / other / no answer

All polled

66%

26%

8%

Republicans

75%

15%

10%

Independents

64%

27%

9%

Democrats

55%

38%

7%

Women

63%

29%

8%

(Afterthought half an hour later – – Pity the poll didn't ask how many would have responded "both".)

Wednesday, September 07, 2005

In response to a comment in an APA I belong to, I made the following comment:

﻿So far, we're not charging more to customers whose water requires more resources to deliver. I imagine a private water utility might be able to implement zoned pricing, with pumped pressure zones being charged for the energy required to pump the water up hill.
And indeed, this would help to discourage people from building on tall hills, and in the long run yield a net savings of energy.
Running the numbers, though, I'm not sure how much of an impact it would have. On average, each person uses 150 gallons of water per day. If we have a 100% efficient pump, it takes 4.65 KWH of power to lift that amount of water 10 feet.
Now, running the numbers, each person uses, on average, 150 gallons of water per day. Lifting that amount of water ten feet takes some 4.65 KWH of power. A pretty good figure for pump efficiency os 50%, so it takes 9.3 KWH to run the pump to lift that water. Figure 10¢ per KWH of electricity, and you're looking at an additional 93¢ per day for every ten feet you have to pump the water uphill. A 100-foot rise would work out to $9.30 per day in additional charges. Fortunately, there are almost certainly intermediate pressure zones in between, so the people at 100 feet would be paying for the lift from those intermediate altitudes. (Maybe they shouldn't?)

Thursday, September 01, 2005

World Net Daily, in a bow to the "Wing Nut Daily" demographic, links to this piece with the headline, "Most Scientific Papers Probably Wrong".

What's going on?

The linked piece, in New Scientist, says, in part:

Assuming that the new paper is itself correct, problems with experimental and statistical methods mean that there is less than a 50% chance that the results of any randomly chosen scientific paper are true.

...continued in full post...

The "experimental and statistical methods" referred to include:

John Ioannidis, an epidemiologist at the University of Ioannina School of Medicine in Greece, says that small sample sizes, poor study design, researcher bias, and selective reporting and other problems combine to make most research findings false. But even large, well-designed studies are not always right, meaning that scientists and the public have to be wary of reported findings.

Traditionally a study is said to be "statistically significant" if the odds are only 1 in 20 that the result could be pure chance. But in a complicated field where there are many potential hypotheses to sift through - such as whether a particular gene influences a particular disease - it is easy to reach false conclusions using this standard. If you test 20 false hypotheses, one of them is likely to show up as true, on average.

Correlation matrices are good at this. A 5X5 correlation matrix will generate 20 numbers you can test for significance. There is a 64% chance that at least one of those 20 correlations will test out as significant, based on pure random chance. If you test the correlations among ten items, there's a 99% chance of finding a publishable result, by pure chance. If you're doing anything like this in your research, you need to correct for it.

Odds get even worse for studies that are too small, studies that find small effects (for example, a drug that works for only 10% of patients), or studies where the protocol and endpoints are poorly defined, allowing researchers to massage their conclusions after the fact.

It's a fact – statistics get "noisier" as sample sizes shrink. The other factor – poorly defined protocol and endpoints – is a big problem, especially in new fields where we're not sure what's happening. In a new field, we're still learning what questions to ask.

However, on a brief scan of the original article, I'm inclined to examine just what the author means by "true". The author uses a figure, the PPV or "positive predictive value", which is the probability that a reported finding is not a false positive. Essentially, it's the probability that attempts to replicate the finding will succeed.

What this paper says is that research results can't be considered written in stone. This is especially true in cases where a field is new, or is hot, or where it's hard to get a large number of observations.

WND likes to group together headlines that relate to broad topics. The link to this article is in a section titled "Evolution Watch". Obviously, this paper is being cited to make the case that evolution is wrong.

The problem is, this paper applies to very specific, new results in the literature. It doesn't apply to findings that have been replicated, as those will have been subjected to better designed tests. It also doesn't apply to theories that are based on large numbers of confirmed findings – the likelihood that all, or even most, of the findings that get incorporated into a theory are wrong is pretty low. It certainly doesn't apply to broad principles that have been worked out over years, decades, or centuries. The likelihood that the laws of thermodynamics are wrong, for example, is incredibly small. The likelihood that evolution as a broad scientific principle is wrong is also vanishingly small.

(I'd be interested to see a study on the odds that a media report on a scientific finding gets it right.)

(Update: I left out a factor of two in the probability calculations. For all the correlations among five variables, there's a 40% chance of a publishable result; and 90% for the ten variable case.)

Lehigh University, the home base of Michael Behe, does not agree with his position.

The department faculty, then, are unequivocal in their support of evolutionary
theory, which has its roots in the seminal work of Charles Darwin and has been
supported by findings accumulated over 140 years. The sole dissenter from
this position, Prof. Michael Behe, is a well-known proponent of “intelligent
design.” While we respect Prof. Behe's right to express his views, they are his
alone and are in no way endorsed by the department. It is our collective
position that intelligent design has no basis in science, has not been tested experimentally, and should not be regarded as scientific.